This study investigated the geochemical behavior and aqueous speciation of rare earth elements (REEs) in the geothermal, cold spring, surface waters, and wall rocks in the Havza (Samsun, Turkey) area. The sampled waters have temperatures ranging from 9.8 to 53 °C, pH values between 6.83 and 8.63, and total dissolved solids between 161 and 665 mg/L. The predominant cations and anions of waters are Ca2+, Na+, and HCO3−ions, respectively. The waters in the study area are generally characterized by Na-HCO3 (SH-5) and/or Ca-HCO3 (ILK, KRK, PNK, CEK, BEK, and TAD) types. All waters are saturated with carbonate minerals such as aragonite, calcite, and dolomite. All waters contain low concentrations of Be, (< 1 µg/L), Cr (< 0.5 µg/L), and Cd (< 0.01 µg/L) contents; whereas high concentrations of Li (3–100 µg/L), Al (2–266 µg/L), Mn (0.2–46.2 µg/L), Cu (0.2–6,2 µg/L), As (0.54–25.1 µg/L), Rb (0.35–16.3 µg/L), Sr (243–1070 µg/L), Y (0.01–36.3 µg/L), Ba (54.2–175 µg/L), V (0.47–5.75 µg/L), W (< 0.02–36.3 µg/L), Mo (0.3–1.2 µg/L), Sb (0.11–0.26 µg/L), Cs (0.003–5.30 µg/L), Pb (0.01–0.88 µg/L), and Sn (< 0.1–0.3 µg/L). Besides, the concentrations of Li, Y, W, Mo, Rb, Sb, As, Cu, Cs, Pb, and Sn are higher in Na-HCO3-type geothermal water than in Ca-HCO3-type waters. Higher Rb/Cs value in cold waters than in geothermal waters is an indication that Cs are retained by clay minerals in the host rocks. Concentrations of ∑REE range from 0.004 to 1.799 µg/L and 2.67 to 121.28 mg/kg for waters and wall rock samples, respectively. In all waters, the concentrations of REE are low and negatively correlated with TDS. The chondrite-normalized REE patterns and Eu anomalies of the studied waters indicate the signature of the host rocks. The speciation of REE complexes indicated that Ln(CO3+) is the major speciation in the alkaline waters, whereas Ln3+ and LnSO4+ complexes form in the near-neutral waters. Thus, carbonate (LnCO3+) complexes were one of the reasons for the enrichment of heavy REEs (HREEs) in alkaline waters. The positive Eu anomalies in some water samples may be indicative of the dissolution of Eu-enriched minerals (clays and plagioclase) or the mobilization of Eu2+ during the water–mineral interaction.